1 Overview of tsRNAsearch analysis comparing TotalRNA versus CytC_IP

1.1 Quantities of ncRNA features identified

1.1.1 Proportions of ncRNA groups identified (normalised by reads per million)

1.1.2 Number of raw reads identified for each ncRNA group

1.2 Venn diagram comparing the three methods used (DESeq2, distribution algorithm, cleavage algorithm)

1.2.1 Details of the intersections can be found here:

  • /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/VennDiagramGeneration/TotalRNA_vs_CytC_IP.intersect…

1.2.2 Files used to generate the Venn Diagram can be found here:

  • /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/VennDiagramGeneration

1.3 Summary Report Table

Top 20 results shown (sorted by distribution score)
feature Fishers.method.pvalue distribution.score DESeq2.Log2FC DESeq2.pvalue DESeq2.padj cleavage.score
ENSMUSG00000093645 (Gm23187) 0e+00 3802095.6 -4.650549 0.0000000 0.0000000 47934.615
ENSMUSG00000065904 (Gm26109) 0e+00 2922939.2 -4.038454 0.0000000 0.0000000 299509.758
ENSMUSG00000080465 (Gm22486) 0e+00 2618347.1 -2.493209 0.0000504 0.0002349 13435.727
ENSMUSG00000088169 (Gm22059) 0e+00 2055911.8 -7.053207 0.0000000 0.0000000 2225.282
ENSMUSG00000095472 (Snord88a) 0e+00 1710839.0 -5.086376 0.0000000 0.0000000 24166.419
ENSMUSG00000065738 (Gm24494) 1e-06 1194959.2 -3.701179 0.0000000 0.0000000 1430180.100
ENSMUSG00000065628 (Snord33) 0e+00 977968.5 -5.697055 0.0000000 0.0000000 261211.204
ENSMUSG00000065735 (Snord80) 0e+00 976233.4 -5.383236 0.0000000 0.0000000 466612.936
ENSMUSG00000104627 (Mir3535) 0e+00 892113.9 -1.915985 0.0010188 0.0036871 55968.391
ENSMUSG00000064778 (Snord59a) 0e+00 827709.5 -5.510282 0.0000000 0.0000000 26989.757
ENSMUSG00000077191 (Snord64) 0e+00 809243.9 -5.659871 0.0000000 0.0000000 13074.825
ENSMUSG00000065281 (Gm24452) 0e+00 793882.9 -3.592234 0.0000000 0.0000000 248493.260
ENSMUSG00000064450 (Snord68) 0e+00 773902.6 -3.873664 0.0000000 0.0000000 526670.399
ENSMUSG00000077527 (Gm25506) 0e+00 758849.2 -5.382228 0.0000000 0.0000000 282819.234
ENSMUSG00000064780 (Snord95) 0e+00 754801.8 -5.438786 0.0000000 0.0000000 204916.346
ENSMUSG00000064612 (Gm26457) 0e+00 732586.7 -2.693973 0.0000005 0.0000033 155982.017
ENSMUSG00000077212 (Snord69) 0e+00 691610.3 -4.226300 0.0000000 0.0000000 866766.671
ENSMUSG00000077493 (Snord91a) 0e+00 683841.7 -3.110862 0.0000000 0.0000000 73479.342
ENSMUSG00000077625 (Snord4a) 0e+00 650475.1 -5.631328 0.0000000 0.0000000 64239.224
ENSMUSG00000064500 (Gm25296) 0e+00 573147.5 -4.792521 0.0000000 0.0000000 375993.038

1.4 tRNA Read Alignment Length

2 Differential Expression Results (DESeq2)

2.1 Overview of DE analysis

2.1.1 Principal Component Analysis (PCA) of all samples

2.1.2 Sample distance matrix

2.1.3 Volcano plot showing differentially expressed genes

2.2 Features identified

2.2.1 Differentially expressed tRNAs

2.2.2 Coverage plots for all differentially expressed tRNAs

2.2.3 Differentially expressed ncRNAs (other than tRNAs)

2.2.4 Coverage plots for all differentially expressed ncRNAs

Full results for features differentially regulated in TotalRNA versus CytC_IP here:

  • /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/DE_Results/DESeq2/TotalRNA_vs_CytC_IP_DESeq2-output.csv
  • /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/DE_Results/DESeq2/TotalRNA_vs_CytC_IP_DESeq2-output-upregulated.csv
  • /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/DE_Results/DESeq2/TotalRNA_vs_CytC_IP_DESeq2-output-downregulated.csv

3 Distribution Algorithm Results

3.1 Feature identified

3.1.1 Highest scoring tRNA fragments identified using the distribution algorithm

Full results here:

  • /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/Distribution_results/TotalRNA_vs_CytC_IP_High-distribution-tsRNAs.txt

3.1.2 Coverage plots for all tRNAs with irregular distribution identified by the distribution algorithm

3.1.3 Highest scoring ncRNA fragments identified using the distribution algorithm

Full results here:

  • /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/Distribution_results/TotalRNA_vs_CytC_IP_High-distribution-ncRNAs.txt

3.1.4 Coverage plots for all ncRNAs with irregular distribution identified by the distribution algorithm

4 Cleavage Algorithm Results

4.1 Features identified

4.1.1 Highest scoring tRNA fragments identified using the cleavage algorithm

Full results here:

  • /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/Cleavage_results/TotalRNA_vs_CytC_IP_High-cleavage-tsRNAs.txt

4.1.2 Coverage plots for all tRNAs with irregular 5’ vs 3’ coverage identified by the cleavage algorithm

4.1.3 Highest scoring ncRNA fragments identified using the cleavage algorithm

Full results here:

  • /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Data/Cleavage_results/TotalRNA_vs_CytC_IP_High-cleavage-ncRNAs.txt

4.1.4 Coverage plots for all ncRNAs with irregular 5’ vs 3’ coverage identified by the cleavage algorithm

5 More results:

5.0.1 tRNA fragments identified where read origin accurate only to isoacceptor level

5.0.2 Features ranked by combined p-value (Fisher’s method)

5.1 Other

5.1.1 All tRNA coverage plots can be found here:

  • /home/paul/Documents/Pipelines/tsRNAsearch/../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin/Plots/TotalRNA_vs_CytC_IP_Features_All-tsRNAs.pdf

5.1.2 Run information

5.1.2.1 Date and time

Pipeline initiated at Mon Nov 18 17:09:56 GMT 2019

Pipeline finished at Mon Nov 18 20:11:21 GMT 2019

5.1.2.2 Parameters used

Parameters:
Species (-s): mouse
Input directory containing fastq/fastq.gz files (-d): ../Miscellaneous-tiRNA-pipeline-stuff/TestData/Mouse-Hyperosmotic-stress-Angiogenin/Data/
Input fastq/fastq.gz file (-f): NA
Experiment layout file (-e): ../Miscellaneous-tiRNA-pipeline-stuff/TestData/Mouse-Hyperosmotic-stress-Angiogenin/Data_Layout.csv
Output directory (-o): ../Analyses_tsRNAsearch/Mouse-Hyperosmotic-stress-Angiogenin
Number of threads used (-t): 40
Plot all features (-A): no
Skip pre-processing (-S): no
Remove intermediate files (-R): yes

5.1.2.3 Version

tsRNAsearch version 0.13.3